Project: Chaos Control
by firewaterwarriorKats
Summary: Sonic and his friends have finally defeated Eggman and his allies once and for all, and now the world is at peace. However, GUN has plans to destroy those much more powerful than they, and set out to capture the four supers. With Sonic gone missing, and the consequences too horrifying to imagine, can the remaining three survive the storm that's fast approaching?
1. Chapter 1: Forecast

**Hello, Everyone! I am so excited to finally share with all of you my new story, Project: Chaos Control! It has been in the works since the beginning of summer, and is still a work in progress. Right now, I am working on Chapter 4 and I will seek to update on a roughly weekly basis, in between school, work and feedback from my betareader, silvershadowlover on deviantart. So, if at any time I don't update around this rough timeframe, don't panic. I may be working on homework or actually working or waiting for feedback, so just keep that in mind. People have lives, you know?**

 **Anyway, here's Chapter 1!**

Project: Chaos Control

Chapter 1

Night stars winked down at the peaceful woodland below, watching with their warm and distant glow as the night owls filled the cool air with their haunting yet melodious songs. A slight breeze caressed the grasses and ferns underneath the leafy canopy, and the daytime wildlife clustered together in their comfy homes as they drifted deep into the realm of sleep. All was well with the world, with nary a soul in sight. At least, that's how it was one mile away from the real story.

A tall tower pierced the night sky, illuminating the clearing underneath and marring the wild beauty surrounding. Alarms blared and sounds of metal banging and screeching could be heard as the top of the tower burst apart to reveal a metal monstrosity. A beast faintly resembling a dragon roared its challenge, its blue and grey colored form framed starkly against the blue-black sky. Its three cold red eyes opened and turned sharply as a glowing gold comet joined it and stared it down.

Super Sonic glared at the powerful robot and clenched a fist. "Face it, Metal Sonic, you're toast! The others are coming and we're gonna smash you into next week!"

"It's **Metal Overlord** , you overrated life form!" The menacing AI raged. "And while the Doctor may be out of commission, your so-called support team will remain busy with the multiple traps I have laid out for them!"

"Oh, really?" Super Sonic replied cockily, glancing back the way he came. Metal Overlord followed his gaze, and if he had a mouth it would be gaping open in shock.

Three more brilliant comets of light burst forth from the ruined tower, two golden like Super Sonic and the third pink and flaming. As the colors came to a stop beside him, it was obvious that the rest of the Emerald-powered support team had arrived: Super Shadow, Super Silver, and Burning Blaze.

Super Sonic grinned and gave them a welcoming thumbs up. "What kept you guys so long?" he joked.

"Hmph! The remaining Black Arms and Mephiles' minions were nothing but nuisances," Super Shadow glowered haughtily.

"As were Nega's forces," Burning Blaze added.

"Also," Silver reported, "Iblis' lava creatures and the Time Eater didn't make things any easier!"

"Ha, says you!"

"What about _you_ , Faker?" Super Shadow smirked. "All _you_ had to do was fight Eggman, Scourge, and Neo Metal Sonic at the same time. Not too much for True Blue to handle, right?"

"Heheh, yeah…" Super Sonic scratched his head. "Well, can you guys give me a hand with Big Blue over here?"

Shadow scoffed. "And here I thought you were gonna save something _challenging_ for us for a change."

"Shut up, Faker."

"Ugh, guys?" Super Silver grunted. "Giant robo-dragon-thing coming this way!"

Sure enough, Metal Overlord took a swipe in the rival hedgehogs' direction, but growled angrily as each one dodged his attack. As the group of super-powered heroes regrouped, they charged their foe with all the elegance and power of warriors in a beautiful dance.

...

As their fight lit up the night sky, elsewhere, a tall figure watched from his office window as he deliberated on the difficult decision he was about to make. After tonight, if all went well, the ones responsible for the spectacular light show would become the most powerful beings on Mobius, if they weren't already. For the human, it was a comfort. To his superiors, however, they were a threat.

A threat that had to be dealt with.

He groaned in anguish as his pen acted of its own accord, signing his name on the section that could do little to spare their lives. Even though he was completely against this new initiative, the political leaders were currently voting on passing the new project, and had pleasantly assured him that experiments were already underway in trying to solve this little...dilemma.

If anyone were to ask his opinion, the situation for the Big Four was surely bleak indeed.

...

The next day, everyone around the world woke up to the news that Dr. Eggman and his villainous allies were finally defeated once and for all. Scourge and Dr. Eggman Nega were sent back to their home worlds under heavy guard. The robots were either dismantled or repurposed, and the Solaris twins Iblis and Mephiles were safely sealed away in separate high security GUN facilities. Dr. Eggman himself was featured on the headlines of every newspaper and news channel worldwide: in handcuffs and glaring at the cameras. Sonic, Shadow, Silver and Blaze were hailed as heroes and honored everywhere they went. The day of their victory became a worldwide holiday, and all the people celebrated as if Christmas had come early. As the sun reached its peak in the bright blue sky three days after that final battle, Sonic and friends found themselves at Tails' house retelling their greatest adventure yet, with Sonic giving everyone a small reenactment.

"...And then Shadow punched his way through the army and all the monsters he touched were thrown high in the sky!" Sonic exclaimed, using a Shadow figurine and a pillow for reference. As he forced the mini model into the pillow, the feathers scattered all over the living room-and among the previously enraptured crowd gathered there.

"Sonic! I just vacuumed!" Tails protested, his namesakes stiff with irritation.

"Ah-choo!" The echidna guardian Knuckles flew back at his powerful sneeze.

"Hey, watch it!" Amy Rose huffed as she shoved the redhead off of herself. She would've given Knuckles a smack on the head with her hammer for good measure had it not been for Cream and Cheese holding her back and imploring her with adorable large eyes.

Silver laughed at the scene, but was punched in the arm by Blaze, who was formally dusting the wayward feathers off of herself.

Shadow watched it all from a distance with his signature impassive frown, wondering whether Rouge was going to show or not. The two weren't overly fond of Sonic's storytelling, but it was a good way to catch up with all their...Well, Shadow wouldn't call them friends just yet, but considered them as such.

The black and red hedgehog heard the familiar ringtone of his comlink as he received an incoming transmission. Stepping outside, he pressed the button allowing the message to play through.

"Shadow? Can you hear me?" Rouge's voice seemed softer and less demanding than normal. Shadow decided to call attention to that.

"Shadow here. What's going on?"

He wasn't sure, but the anti-hero thought he heard a strange sadness in her tone.

"Remember the GUN policy update the superiors were deliberating over last night? Well... they approved Project: Chaos Control."

...

Sonic the Hedgehog wasn't one to stay after a party and clean up. Especially when a certain hot-headed echidna was responsible for most of the mess, trying to punch a certain blue hedgehog in the face. And so, with the excuse of needing some fresh air, the blue blur took off.

Tails and the others grumbled about the hero's untimely absence.

"Just like back with Perfect Chaos," Amy sighed, sweeping the living room floor.

"Ooh, was that when the city was flooded?" Silver asked eagerly. He was tasked with picking up and putting things back in their proper places.

"Yeah," Tails replied, sorting out the scattered tools. "How'd you know?"

"Silver loves history," Blaze put in with a smile. "How else did you think he found out about the massive Eggman alliance?"

Everyone smiled at that. No one had seen the alliance coming; if it weren't for Silver's warning, things would've ended very differently.

Knuckles suddenly frowned at a new thought. "Does that mean you'll be leaving soon?"

Silver's quills noticeably drooped. "Yeah, my time here is over."

"And so is mine," Blaze stated. "The people of my world would probably be expecting me home by now."

"Oh, that's too bad," Cream sighed. "Please come visit us soon, okay?"

Blaze smiled at the young rabbit, a budding warmth flowing through her senses. "Don't worry, it's a promise. And maybe next time, I'll bring Marine with me."

"That would be wonderful!" Cream cheered, followed by her companion Cheese the Chao's chirrup of approval.

Just then, Shadow burst through the front door, looking for something. When his eyes fell on Silver and Blaze, he rushed up to them and grabbed each of them by a wrist. "We need to get going, _now_." He grunted urgently, pulling them toward the door. "Where's Sonic?"

"Woah, wait Shadow," Silver protested, pulling against the anti-hero's hold as Tails blocked his way to the door. "What's going on? Sonic went for a run."

"Stupid Faker," Shadow cursed, shoving his way past the two-tailed fox. "He's gonna get himself captured and smuggled into GUN's hands…"

"Shadow!" Blaze lit up her hands. The dark hedgehog gave a low hiss and let go of the princess's wrist, but before he could retaliate, he found himself trapped in a teal glow. "This is ridiculous! Tell us what is going on! What danger is Sonic in, and what does it have to do with us?"

The Ultimate Lifeform growled at finding himself in such a vulnerable position, but seeing that the younger heroes wouldn't be satisfied without an answer, he sighed and let go of Silver's wrist.

"GUN cast a vote for an initiative called Project: Chaos Control. They passed it, and now all the people able to achieve a Super form are in danger."

 **Suspense! How we writers _love_ to leave the audience with cliffhangers! **

**So how was it? Good? Needs improvement? Reviews are appreciated!**


	2. Chapter 2: Consequences

**Hello again, and here is the much-anticipated Chapter 2!**

 **WARNING: For those sensitive to torture scenes and the like, please do not read the section after Sonic! This is a major reason why this story is rated T, along with a few character deaths. Tread with caution!**

 **Anyway, enjoy!**

Project: Chaos Control

Chapter 2

Rouge crouched in the shadows, just one Mobian hidden among a sea of Mobian and human news reporters under the steel roof of the Guardian Units of the Nations' main news conference building. She was positioned near the front rows of the assembly, off to the side and away from prying eyes as any professional spy would place herself. At the moment, the seductive bat wasn't hiding for the sake of glittering jewels, as she usually was. No, she was here and well concealed in order to gather more information on Project: Chaos Control.

Just as she whipped out her wireless search engine for GUN's files, the jewel Huntress's highly-sensitive ears pricked up as she detected the telltale footfalls of the region's top GUN official. The last-minute shuffling and murmurs of the reporters overpowered all other sounds, but Rouge didn't care; in fact, she welcomed the sound cover. This mission was too important to be bothered by annoying noises. The stakes were simply too high, as her partner would attest…

...

Said partner to Rouge the Bat pushed away the thick branches that obscured the hidden path through the forest, growling under his breath at the multitude of burrs stuck to his fur. Following close behind him were the two youngest Supers, Silver and Blaze, and Tails the kid genius. The GUN agent had insisted they come out to these woods to make sure they could talk without being listened in on. Also, Shadow concluded that if GUN were looking for the four Supers, Tails' workshop would be the first place they would look.

And if one of them were to get captured under his watch…

Shadow shook his head, refocusing on his current task. He couldn't afford to let these thoughts trouble him; he was the Ultimate Lifeform, for Chaos' sake. If anyone could keep the Supers safe, it would be him.

At last, the small group reached their destination: a small clearing with fallen logs arranged in a circle. The waning afternoon sun filtered in through the leafy overhead canopy, and the sound of the forest rodents filled the surrounding trees with their hustle and bustle.

Shadow turned and seated himself on the log to his left. The other three proceeded to occupy the other log across from the GUN agent.

Shadow cleared his throat. "As you know, since our final battle with Eggman and his allies, all of our previous foes were defeated and locked away. Even Mephiles the Dark, who otherwise would've slipped away in time, is finally contained and grounded in this present. However, certain international officials found it worrisome that our... connection to Chaos energy remains unchecked. Without any major threats to the world at large, we are the most powerful beings on Mobius. To the world, we are it's protectors; but to the nations, we are their greatest threat."

"And so this... initiative was born," Blaze nodded in understanding.

"Yeah, but why?" Silver asked. "They have the latest technology of this time and an army. Why should they be afraid of us?"

Blaze arched an eyebrow. "Remember Solaris?"

"...Point taken."

Tails, having not said a word since their short trip here, suddenly looked concerned. "Shadow, how exactly would GUN solve this...problem?"

The Ultimate Lifeform turned away, not wanting to convey the awful truth behind the name but knowing he had to anyway. "In essence? They would destroy the Super form."

...

Sonic raced through the field, his worries long since lost to the thrill and freedom of being able to run. The ground blurred beneath him, and the world seemed to stretch out before him as if welcoming him into its bosom. The Blue Blur leapt off of a cliff and seemed to glide back down to earth, one piece of carefree sky come to grace the world with his wondrous abilities.

This was what he was, this was what he lived for. Sonic the Hedgehog, fastest thing alive, as wind incarnate.

...

Blackness and depression hovered over his head like a black cloud, heavy and robbing him of the peace in being left alone. His intelligent mind forbade him from seeing any good come out of his current situation.

Ever since the Big Four defeated Eggman and his allies, his life had been a living hell. He was closely monitored at all times, always watched yet never acknowledged, denied even the privilege of morphing into his base form. He was stuck in the now humiliating Shadow doppelganger form, and it was all he could do not to retaliate against his tormentors.

Still, at least he still had his brother, Iblis. Even if they were separated, at least he knew he wasn't sealed away in another annoying princess like last time.

He flinched in surprise at the sudden sound of his cell door opening, growling low as they tried to creep up behind his turned back. As they drew closer, the shade swiftly ducked under them and made for the open door, half hoping for one of them to come after them so he could have an excuse to seriously harm them.

Unfortunately, the ankle chain bolted to the floor grew taut and tripped him up, allowing for the soldiers to swiftly pin him down. He spat out a string of curses at his assailants as they handcuffed his hands behind him and clipped on long poles to his inhibitor collar.

"You insolent mortals! Unhand me this instant!"

"Quiet, darkling!" The soldier in charge barked back, taking out a small remote and pressing the single button. The shade howled in pain as his collar activated and shot several volts of electricity into his veins, leaving him quivering uncontrollably on the floor.

"Talk back again and I'll make sure you're unconscious next time," the soldier retorted, more annoyed than angry at the glare he received back. "Take him down to the lab."

Making sure the poles were completely taut between them, the small convoy of soldiers half dragged half prodded the shade down the corridor and into the elevator, snickering as he stumbled over his feet. All he could really do about it was glare hatefully at them as they waited in the elevator in silence, broken only by the chime that indicated their descent into the basement level floors. Once the contraption opened its doors, the soldiers dragged him into the most feared floor in the facility.

The lab was harsh and glaringly bright white, so much so that the dark being had to squint his eyes in order to see. Each scientist was outfitted with GUN lab uniforms, all clinical and cold to their current subject. In the center of the floor, as if an altar to their god of science, hummed their most prized invention-and the reason for him being there.

He pulled against his restraints as they continued to drag him to the machine. He spat out empty threats and dug in his heels, but their hold on him was unbreaking; they seemed to have heard the same song and tune.

He was outraged. How dare they ignore him and treat him like an uncomplacent pet they must drag along? He was the demon of time, for Solaris' sake!

The closer they got, the more frantic his efforts became. Something didn't feel right about the machine he was being dragged to like a bull to the altar; he felt some Chaos energy in there, but it was...off. More negative and volatile, as if it would tear his insides apart if it could. He continued to thrash and curse and caterwaul, mentally crying out for his twin.

Of course, there was no answer.

For the first time, the shade felt utterly powerless. Though he demanded they leave, the soldiers continued to guide him towards their altar/god. He couldn't even fight back, for his powers were cut off from him and he limbs were tightly restrained. Even if he could fight back, all he would earn was a painful electrocution and it wouldn't even change his circumstance.

As the demon of time, he was used to changing circumstances and altering fate. He had used that advantage against his opponents since his release from the Sceptre of Darkness, from preventing the complete annihilation of himself and his brother to battling with Shadow in this last skirmish; no matter what anyone would say, it was an integral part of who he was as the demon of time. To have that freedom and ability stripped from him was...demoralizing. Utterly humiliating.

At last they were before the machine. They tied him hand and foot to the lone chair with rough and unsympathetic hands, ignoring the fact that his ears were flattened to his head and his tail was between his legs. They sealed him inside the container, muffling the sounds outside and decidedly overlooking his hate filled and somewhat fearful demeanor as the head scientist read aloud this session's information in a low and dull voice that barely reached his test subject's ears.

"Project: Chaos Control. Subject: Me...les... Dark. Experiment...7. ...pm. First attempt...inhibit...Chaos energy use without inhibitors."

"...Probes... in position," one of the lower level scientists droned from behind his computer screen.

"...Weapon's charged. Ready… command."

"..."

He tried to hold back his screams as waves of pain flowed throughout his body like hot lava, brought by several volts of what could only be described as negative Chaos energy and lightning mixed together and trapped in this glass prison. His head seemed to be being pierced by thousands of nails being hammered into his skull by multiple mallets, all swinging in unison. He held in the sound of his torment for as long as he could, until he couldn't hold it back anymore and numbly felt it release of its own accord. His sight became fuzzy and distorted, and all sound, even his own screams, became lost in one melded buzzing noise overpowering his senses.

His body spasmed uncontrollably underneath his restraints as the pain continued its destructive work with no end in sight. He tried to reach out to his twin, but as he did, the pain in his head intensified twofold. He arched his back and howled in renewed torment as his first hot tears dripped down from his reptilian eyes and left wet marks on his grey-black legs. He thrashed around, screaming hate and defiance until he couldn't take anymore. The world seemed to swirl in further distortion, shatter like glass, then disappear behind a thick veil of unbroken darkness.

...

 **(Takes deep breath) Man, this ending made me depressed after writing. There are some moments in writing when it seems like the lines between author and character are blurred, and this was definitely one of those rare moments. I don't believe I will ever see Mephiles the Dark, one of the best villains in the Sonic franchise, the same way again...**

 **Hope you enjoyed this chapter! Please, R & R!**


	3. Chapter 3: Capture

**Hello! Just as an update, I decided I will be updating this story on a roughly biweekly basis, just because I have to balance my time between work, school and writing, and at the moment that balance is shaky at best. But, like I promised, here's Chapter 3!**

Project: Chaos Control

Chapter 3

The world seemed to stop. Silence reigned in the clearing in the middle of the forest at the Ultimate Lifeform's last statement. Those gathered could barely utter a sound as the very idea of what they just heard struggled to enter their stunned minds.

"Wh-what?" Silver stuttered.

"Destroy the super form…?" Blaze asked to no one in particular.

"How can this be?!" Tails burst in outrage. "After everything you guys did to save the world multiple times over, and they want to take away the very thing that… that… That's so cowardly of them!"

Shadow tried hard not to let his emotions break through the calm and collected demeanor he was trying to project for the sake of the younger three, but all took notice of the furrowing of his eyebrows, the only sign of worry to make it past his defenses.

"It's difficult to accept, I know, but this is the reality we now face. GUN has betrayed us, and I have no doubt that they will promptly hunt us down before the end of the day."

"Then we'll go back to my time!" Silver blurted out. "They may forget about us by then; we'll be safe there! Wait; then, I mean," he added embarrassedly.

Shadow was already shaking his head by the time the naive hedgehog was finished.

"I highly doubt they will. They possess the latest technology and keep meticulous records of everything and everyone-even citizens. Even if people forget, the databases won't."

"What about my dimension?" Blaze suggested. "As the princess of my world, I have the authority to shelter refugees in need."

"GUN has set up a series of satellites built specifically for preventing dimensional gateways from opening to other worlds," Shadow explained. "I have to give them credit; they truly were prepared in case something like this were to happen."

"They must have planned for Project: Chaos Control for a long time," Tails speculated. "There's no way they could have built an _entire network_ of satellites dedicated to preventing interdimensional travel outside of our world _and_ gather the resources necessary to carry out such an operation in _three days_! Even for a genius inventor such as myself, it would take such a long time to simply get all those resources, nevermind assembling them!"

"So essentially, we're stuck," Blaze summed up.

"Yes," Shadow confirmed somberly. "Yes we are."

A familiar ringtone shattered the tense atmosphere, making the gathered heroes jump in surprise. Shadow glanced at his comlink, recognizing the caller, and opened his end of the transmission.

"Ebony to Ivory. What's your status on Project: Chaos Control?"

"Not good," the voice belonging to none other than Rouge the Bat filled the clearing with the urgency of her message. "Do you have the other three with you?"

"The youngest ones, yes," Shadow replied. "That blue Faker is nowhere to be found."

"Drat," Rouge cursed. "Shadow, you have to find him, _now._ GUN is making its move."

...

The Great Forest swayed under the soothing lullaby of the evening breeze, it's picturesque calm broken only by the sound of the world-renowned Blue Blur as he took a high-speed stroll through its protective canopy of leafy green ferns. The hero leapt from the tree trunks at speeds only he could fathom, and shot onward much faster than a speeding bullet could only hope to achieve. At last, the speedy blue hedgehog made a massive leap on a log perfectly positioned for a high-speed jumping board, performed multiple flips and tricks in the air, then landed perfectly in a little section of forest whose canopy opened up to reveal a small patch of wildflowers drinking in the last evening sunlight.

The speedster glanced at his comlink which doubled as a timer. "Hmm, one minute and forty-five seconds from Hidden Palace to the Great Forest. That's gotta be a new record!"

As if on cue, his comlink beeped and revealed his score on this run.

"Rank B?! You gotta be kidding me?!"

Again, his comlink beeped, but following it was the F.U.N. Song ringtone that he had assigned for one specific faker…

"Sonic! Where the hell are you?!"

"Oh, hey Faker. Calling for a rematch?"

"No, I'm not-"

"Well, **I'm** asking for one. You totally cheated during the last leg of Green Hill Zone!"

"No I did-Sigh. Sonic, you need to get back here, **now**. I can't tell you over the com, but GUN is planning something dangerous and they're possibly hot on your trail as we speak-"

"Yo, Shads, I **got** this. You just take care of the others and I'll be over-Augh!" The Blue Blur cried out in surprise and pain as something implanted itself in his back, generating enough electricity to knock him into the ground, unable to move aside from the spasms that wracked his body.

"Sonic? _Sonic_!" Shadow's voice yelled from the comlink before the electricity cut off the transmission and forced the device into shutdown mode. Despite his paralysis, Sonic could hear multiple soldiers closing in, surrounding him on all sides.

In that moment, the Blue Blur knew he was chest-deep in some serious trouble.

...

"Sonic? _Sonic_!" Shadow yelled into his comlink before static overtook the other line. He cursed sharply and threw the useless device far from the clearing, his face a mask of rage with underlying agitation glistening in his ruby-red eyes.

"I'm going after him," he stated, determination strengthening his resolve. He took out the red Chaos Emerald he always carried with him and raised it high over his head, glancing back at the three younger heroes.

"Tails, go home. GUN will visit, and we need you to cover for us in case they come asking questions. Silver, Blaze, you two stay here and keep each other safe. Don't leave the area and _don't let yourselves get caught_! Understood?"

Then, without bothering to wait for an answer, he shouted "Chaos Control!" and vanished in a flash of white.

...

When the light faded, the Ultimate Lifeform found himself in the same clearing where Sonic had been, only the wildflowers bore the scars of some struggle that had taken place there not too long ago. He noticed that all the signs were within the patch of wildflowers; nothing else seemed affected or showed anything remotely similar to a human-sized or Mobian-sized footprint to follow.

As his gaze swept over the scene, the glint of something metal caught his eye. He crept up on the mystery object slowly, careful in case this was a trap. As he drew closer, he recognized the object as Sonic's comlink, only now it was cracked and very much broken. He gently picked it up, stared into the broken face where Sonic had last seen his face and heard his voice…

Shadow didn't even notice he had fallen to his knees, and even if he did, he refused to care. All he could think about was his latest and most devastating failure since Maria's death as he proclaimed his rage and shame at the rapidly darkening sky.

Once again, he had failed a dear friend.

...

An hour later found Sonic being dragged down a corridor in a secret GUN facility, hands and feet bound with cold metal shackles. He couldn't see out of the sack they had thrown over his head, and his efforts to gain information were only met with either steely silence or prodding with nasty stun batons. He clenched his teeth, angry at himself for letting his guard down, and angry at GUN for the violent attack. They could've at least given him a thumbs up about their little visit _before_ they stunned him into submission.

At last, they seemed to have stopped. He heard a soldier take something out and slide it against something, then pricked his ears at the sound of a heavy metal door sliding open with relative ease. The hands that held his arms jerked him roughly beyond the metal door, and held him in place as a second soldier attached an ankle chain to his right leg and an inhibitor collar around his neck.

Finally, they tore the sack away, and Sonic blinked his emerald green eyes as he tried to adjust to the brightness of the room he now found himself in. It was bare and small, with only a steel bench almost as long as the wall bolted to it for resting or sleeping. A single blanket and pillow lay on the right side of bench, and as he glanced at his steel tether, he realized the end of the chain was securely bolted to the floor. The light was bright enough to illuminate his form, and even as he blinked, he could just barely make out the faces hidden behind the GUN standard helmet and facemask.

"Hey, you guys know why I'm here?"

"Quiet!" The soldier holding him spat, reaching for his stun baton.

"Soldier," the other one sternly said. "Put that away. He has a right to ask."

The first one grumbled something under his breath before he reluctantly complied, reaching instead for the keys to the hedgehog's shackles. He unlocked first his hands, then his feet, and walked away to stand beside his superior as the blue blur stood up and faced his captors.

"Are you guys gonna tell me why you had to kidnap me?"

"Sorry, Blue Blur, but we are under strict orders not to tell you anything other than this is only temporary and that you will be released as soon as GUN is finished with you."

Sonic raised an eyebrow. "Finished with me...how?"

"That's classified," the superior snapped abruptly, motioning for his partner to follow him out of the cell. The metal door, it's only feature a small plexiglass window, opened for them and the two slid out.

"I hate seeing you like this, Blue Blur," the superior sighed, oblivious to his partner's presence beside him. "If it were up to me, I wouldn't have let them take you-" Whatever he had wanted to say was cut short by the automatic door, and Sonic found himself all alone-and in a confined space.

He started to breathe heavily as it seemed that the walls began to close in on him, chipping away at the space and trapping him further in their cold embrace-

"Can't you hyperventilate and whine **quietly**?" A muffled voice snapped from a neighboring cell, annoyance clearly scalding in its tone. "I barely get enough sleep as it is!"

Sonic tensed at the voice, recognition widening his emerald green eyes in shock.

 _No, it couldn't be..._

He walked toward the right corner of his cell, seated himself on the bench, and turned toward his new neighbor-and former foe.

"Mephiles?"

 **P.S. if you write a review or PM me anytime this weekend, it may be a while for me to reply because I will be on vacation and there will be NO WIFI! So, sorry in advance and just be patient; I will get to you as soon as I get back on Monday.**

 **In the meantime, hope you enjoy!**


	4. Chapter 4: Confessions

**Hello, everyone! I have decided to spoil you guys and give you Chapter 4 early! So, without further ado...**

Project: Chaos Control

Chapter 4

Blaze slowly blinked her golden amber eyes, musing over the new Mobius she was now trapped in. In front of her, Silver paced restlessly, mind otherwise occupied. His hunched shoulders and clenched fists gave away the fact that he was most likely thinking about Sonic and Shadow.

It had been almost a half-hour since Shadow had left to try and save Sonic, and neither of the two had seen nor heard a sign of him since his Chaos Control. Tails had long since left in order to cover for them in case GUN showed up back at the workshop, but even the kid genius' assurances may not be enough to get the military off of their trail.

"I'm going after them."

Silver's declaration snapped Blaze out of her thoughts, renewed concern hidden under her calm demeanor as she looked at her friend. The silvery hedgehog stood tall, confident in his decision. The determined glint in his golden eyes only served to show how naive he was to think he could find the two fastest things alive.

"Silver, no," the pyrokinetic feline said, rising from the log. "You don't know where they are or where Shadow Chaos Controlled to. How exactly are you going to find them?"

Silver looked taken aback at his companion's response. "Um, I'll just use Chaos Control, to send me to where they are now."

"But what if they're in a battle with GUN? What would you do if you were suddenly surrounded by the enemy?"

"Just psychokinesis them in the butt and-"

"And if it turns out GUN has captured them?"

Finally, Silver was at a loss for how to respond to Blaze's counter. She sighed heavily as the time traveler scratched his head.

"Silver, you're so naive," she murmured. "We don't have a chance at finding them on our own, not without knowing where Shadow Chaos Controlled to. Right now, the best thing we can do is stay here and be on guard in case GUN arrives."

Silver said nothing for a moment, still digesting what Blaze was saying. Then he turned his head and gazed at her fondly, a small smile playing with his features.

"Maybe you're right," he admitted. "I mean, Shadow's a smart guy, I'm sure he's gonna be fine no matter what-"

" _Get down_!"

Blaze obeyed that familiar growl and threw herself onto the ground, realizing that she had been close to becoming GUN's second victim as she tracked the stun bullet that whizzed by where she had been standing only a second before. She rolled toward Silver, who had been thrown into the ground by none other than Shadow, and all three took refuge behind one of the logs.

"They already found us?!" Silver exclaimed, ducking his head as another stun bullet whizzed by overhead.

"They were tracking our Chaos Energy signatures," the Ultimate Lifeform growled, anger fully displayed on his dark face.

"Where's Sonic?" Blaze asked, noticing the fact that there were only three of them.

Shadow face, if it hadn't been serious before, certainly looked grim now.

"I was too late to save him," he snarled, his rage directed to no one but himself. "And we'll be joining him unless we can get to someplace safe, somewhere where Chaos Energy signatures can be masked or muddled. Someplace like…"

His ruby eyes eyes widened at a sudden revelation. Blaze tipped her head, curious, before having to be forced down again as another bullet among the hail of gunfire aimed itself for her head.

"What do you have in mind?" She yelled over the thundering noise.

"There's a place we can retreat to for now," Shadow replied, a new commanding tone taking its place over his previous anger. "Silver, give me your Chaos Emerald. Blaze, hold on to him and myself."

Both younger heroes complied with the Ultimate Lifeform's request, each one glancing at the other before holding hands. Once Blaze grabbed a hold of Shadow's black and red arm, the former GUN agent held the yellow Chaos Emerald high in the air.

"Stop him!" A soldier cried out, but he was promptly cut off by two dreaded words.

"Chaos Control!"

The soldiers shielded themselves from the blinding light that followed, and when they dared to look up, they were angered to discover that their quarry had escaped.

...

"Mephiles? Is that you?" Sonic listened intently from his side of the cell wall, rewarded for his inquiry by a deep voice that could only belong to one villain.

"Yes, but why are you here?" If Sonic had been able to see his cell neighbor, he would notice the shadow's head was tipped in confusion and curiosity. "I thought I was the only one here."

The hero of Mobius shrugged casually, tossing the soldiers' grim attitudes out of mind.

"Ehh, I dunno, to be honest. Somethin' 'bout a temporary thing or whatever. They said they're gonna let me go soon after whatever GUN wants with me. Although, they didn't need to, like, kidnap me in the first place," he added with frustration, glaring at the door they had exited his cell from.

"You do realize that they took you for a reason?" Mephiles tapped his gloved hands on the wall, deep in thought. "They don't do anything without a good reason. And if they had to take you by force…"

"Whatcha thinkin', Faker Number Two?"Sonic tried to joke, but was cut off by the shade's sudden inquiry.

"Do you know what Project: Chaos Control is about?"

Surprised, the blue hedgehog found himself caught off-guard. "Never heard of it. Faker Number One said something along the lines of 'GUN planning something dangerous, onomatopoeia' before our comms got jammed."

"He got to you too late," Mephiles' growling voice could barely be heard on Sonic's side, and so he pressed himself against the wall in order to hear what he had to say.

"Sonic, they are going to destroy everything that defines you, every ounce of Chaos energy you have in that mortal body of yours-even your speed. Had my loathsome rival gotten to you sooner, you could have been spared from the horror of the new reality that now awaits you. However…"

"He was too late," Sonic finished, for the first time feeling an impending sense of dread and despair wash over him. Refusing to give in, he shook himself off...and noticed a new change in tone from his new neighbor.

He turned to face the wall. "Sounds like the same thing happened to you."

The Blue Blur heard the shade scoff as he gave his reply. "You barely realized that now? I could have appeared to you from the shadows of your cell if I could use my abilities. I could have blasted through this wall that divides us, killing you in the process just for spite. For Solaris' sake, I could have called for my brother, Iblis to appear and burn this entire facility to ashes! But they took _everything_ that would define me. _Everything_ that made me the intelligent half of Solaris, a manipulator of the shadows, the one even the great _Shadow the Hedgehog_ cannot take lightly! And now it is all _gone_! They took away my brother, locked away like the caged animal he is not! They took away my ability to travel through time! And now they took my ability to fuse with Iblis and become Solaris! They stole my identity! They destroyed a deity! They. Ruined. _Everything_!"

...

Silence settled itself between the two hedgehogs as a dove would in its nest, neither one daring to say a word after that sudden outburst.

...

Mephiles staggered back, cursing himself for saying so much. He had only intended to say enough to scare the speedy blue imbecile into a blubbering fool, but now it seemed he had exposed himself to a humiliating degree. And to a sworn enemy, no less!

 _Curse GUN and their cruelty,_ he thought bitterly, wishing he could form an energy orb for the sole purpose of releasing his pent up anger and frustration. _If they hadn't resorted to manipulating that Chaos Energy for their own personal gain, then perhaps there could have been-_

He shook his head suddenly, and laughed to himself at a new train of thought. _No, I could never be like them. I was wrongfully sealed away barely a half hour after my birth, left to rot in the unending blackness of which defines me. Then, after a decade of tormenting nothingness, the very one who drove me to insanity magically forgets I even existed! All of my hate, all of my preparation for our possible reunion, utterly wasted because of that time paradox! I never had a choice as far as my fate, yet_ they _choose to take it from others, my sworn enemies even! Though I may see some satisfaction in their suffering, not even I would wish such tormenting punishment upon anyone else… not even Shadow the Hedgehog…_

That last thought surprised him more than anything else. That hedgehog was responsible for creating the Mephiles everyone knew; and while the shade wanted desperately to see him encounter some form of punishment as a result of his actions that fateful day, ultimately, no retaliation or consequence in all the world could change those events-and neither could he. Now that he could never be able to travel through time again…

"Mephiles." The sound of the Blue Blur's voice snapped him out of his reverie. "I'm really sorry that happened to you. If I had known this would happen, I would've never-"

"Save your pity for yourself, hedgehog," Mephiles snapped, whipping his head to face the wall. If that speedy blue imbecile could see him, he would be taken aback by the bristled quills and clenched fists that displayed the shade's hostility.

"Soon enough, you will become their next victim, and all that defines who you are will be taken from you. Once that happens and you are released into the world, you will count your blessings, and be thankful that you are not a monster like me. I am far from deserving any sympathy from you, or anyone else in this rotten world we live in.

"...You best get some rest," the intelligent half of Solaris suggested, deciding to cut the one-way conversation short. "Once they come for you, you will need all the strength you can muster to face this devastating trial before you. Once you leave, you are to tell no one about our... conversation."

"Heh, no biggie," the blue hedgehog replied from his cell. "Your secret's safe with me!"

...

Sleep came surprisingly easy for Sonic, which couldn't be said about his cell neighbor. Throughout the night-or was it day?-he had heard the shade constantly fidgeting and pacing, often talking to himself about something distressing or frustrating to his one-hedgehog audience without revealing his secret struggle to the other prisoner. The Blue Blur, though somewhat disturbed by the new Mephiles he was listening to, decided to put aside that problem for the morning-or was it night? He couldn't tell for sure, since he had a terrible sense of time…

Footsteps outside of the cell door prompted Sonic to sit up on his sleeping bench just as the metallic contraption slid open to reveal a small group of soldiers-and one grim-faced commander.

"Commander Tower?" Sonic certainly wasn't expecting this GUN official here, not after what his soldiers did to him. If there weren't so many of them here, he would've Spin Dashed the human into the wall and given him a piece of his mind-

"Sonic the Hedgehog," the older human replied, taking a few steps into the cell. "It's time for your procedure."

 **Well, that was interesting! Sonic is adorable as ever, especially when he gives Mephy the nickname of Faker Number 2. He's perhaps one of my favorite characters to write!**

 **Anyway, Chapter 5 will probably take a little longer to update because a lot of plot stuff happens then. So, just be patient as I work on one of the most important parts of the story. Trust me, you won't see what's coming (Mwahahahaha!).**

 **(Ahem). Till then, hope you enjoyed! Please leave a review, it helps a lot!**


	5. Chapter 5: Awakening

**At last! I was so excited to finally get to this part of the story, mainly because I want to get on with the rest of the plot (and believe me, there's a lot of plot). This is perhaps the biggest chapter so far, so I hope you're ready to get comfy because lots of stuff is going down!**

 **WARNING (and mild spoilers): Someone dies this chapter. Not saying who (if I told you, that would be a major spoiler), but if you don't want to read the details, then start skipping after the dialogue starting with "Yes... and no" and continue reading at the dialogue that starts with "Y-you killed him!" Thanks!**

 **Now, without further ado, enjoy the many twists this chapter has to offer!**

Project: Chaos Control

Chapter 5

Once the flash of light faded, Shadow the Hedgehog finally allowed himself an exhale of relief. Behind him, the younger two Supers let go of each other and took in their new surroundings.

Their refuge was dark and poorly lit, with patches of blue-white light coming from the overhead lightbulbs. The black and red leader turned to the wall behind him and after a short time of feeling the surface flipped a switch.

Instantly, the room became bathed in warm light. It appeared they had Chaos Controlled into a main computer room, the multiple screens blank for the moment.

Shadow walked up to the lone console.

"Where are we?" Silver asked, a slight nervous wobble in his voice.

"We're currently in one of many secret bunkers," Shadow replied, starting up the computer. With a small whirring sound, the machine came to life, displaying a loading screen in the shape of…

"Isn't that Eggman's logo?" Blaze questioned, alarm flashing through her pelt. Silver, realizing the same fact, glanced around them, expecting some sort of sudden attack. Instead, a monotone female voice responded.

"Scanning life forms… Welcome, Shadow the Hedgehog. Salutations, Silver the Hedgehog and Princess Blaze the Cat."

"E.V.E., restart all security programs and defenses. Block all contact attempts by GUN and activate all forms of cloaking."

"Acknowledged. Defenses online."

With a barely discernible hum, warm light flooded the room and the rest of the abandoned base, serving to welcome its new inhabitants. Security cameras came online once more, their recordings now displayed throughout some of the screens. The threesome watched as hallways, storage rooms, a small clinic, and even the battered remains of a robot factory finally saw the light. Dust was everywhere, but it might as well be nonexistent in the eyes of the three who sought a sanctuary-and found it.

Silver and Blaze shared a relieved and proud glance before turning to Shadow. The Ultimate Lifeform stood hunched over the control panel, allowing himself a small moment of grief over his failure to save Sonic, before pulling up a chair and seating himself.

"We're not out of danger yet," he stated simply. "We may have a safe place to stay for now, but I am willing to bet the Doctor didn't plan on ever returning to this place. We won't do ourselves any good leaving for supplies without some sort of cloaking device, but neither is rotting here with nothing a good idea."

Silver knitted his brow, at a loss for what to suggest to solve their new dilemma. Blaze, as well, couldn't think of any solutions.

Then, a four-note ringtone filled the silence and EVE's robotic voice provided the answer to its question.

"Incoming call from unknown source. Signal coming from: Tails' Workshop. Would you like to take it?"

"Yes," Shadow answered, mildly surprised that the young genius had figured out where they were hiding so fast. Static flickered on the main screen, but was soon replaced by the face of a yellow fox with sky blue eyes.

"Hello? Shadow?"

"Tails," the Ultimate Lifeform spoke. "How did you find us?"

"Well," Tails scratched the back of his head shyly. "Rouge told me about the secret bunkers and I've been calling each one for the last half-hour using the Miles Electric. Is everyone alright? Where's Sonic?"

Shadow clenched his fists and gritted his teeth, not daring to look the young fox in the eyes. "I was too late. GUN has him."

Tails blinked, trying to hold back the sudden wave of tears that threatened to fall. Sniffling, he tried not to dwell on the news and his brother's possible fate as he remembered why he was calling them.

"Shadow, Rouge wanted me to tell you something important. Turn on the news."

...

Sonic faced the GUN commander with his trademark confidence, successfully hiding the anxiety that threatened to break through to his supposed enemy. He hopped down from the bench, waiting for something to happen. Instead, Commander Tower glanced away from the speedy blue hero.

"I trust you will come quietly, unlike certain others?"

Sonic gritted his teeth, knowing who the "certain other" the Commander was referring to.

"You never had to hurt him like that," he stated, glaring at the soldiers. Some returned his gaze, unrepentant, while others looked away.

"Unfortunately, it was necessary for the sake of the project," Tower replied smoothly. "Besides, we can both acknowledge that power over time should never be left in the hands of any one person, especially one like _him_."

Sonic winced slightly at the sting of that last remark, even if it hadn't been aimed at him. _Is that what the Commander thinks about the rest of us? Too powerful to be left alone?_

The older human turned to two to the soldiers and nodded. Wordlessly, they entered the cell and made their way towards the trapped hedgehog with handcuffs at the ready.

Sonic stepped back threateningly. "Aw, Hell no. You're not putting those on me again."

"Sonic," Tower warned.

"No! Let me walk, at least, please?" the blue blur pleaded.

There was a moment of silence before Tower gave his reply. "If we do this, do you promise you won't try to escape?"

The speedy blue hedgehog gave him his trademark smirk and a thumbs up. "Heh, no problem."

"Very well," the Commander turned to the soldiers. "Just his hands."

The two nodded and complied, securing the hedgehog's hands behind him and unlocking his tether before guiding him to the door. The rest of the soldiers instantly snapped to formation, positioning themselves so that the world's hero was surrounded on all sides. Commander Tower stood at the head of the escort as they started down the hallway and towards the elevator.

Sonic glanced at the cell door next to his own, glaring at the plexiglass window just a head taller than him. He was sure Mephiles had heard the entire conversation. Whether the shade was gloating over his coming trial or still talking to himself was uncertain.

They continued the procession in silence, something that disturbed Sonic greatly and did nothing to ease the anxiety in his chest. And so, he decided to do something about that.

"So, what's gonna happen next?"

The GUN commander hesitated as he pressed the elevator button, wondering if he was authorized to give any information, then decided to uncharacteristically screw protocol and answer the hero's inquiry.

"First, we're taking you to the lab to have some of your Chaos Energy removed, alter its nature to act as an inhibitor, then return it. After that, you will stay here for a few days to recover, as the process does inflicts some pain, and then you will be released."

Sonic and the rest of the escort entered the open elevator. The Blue Blur was glad he had managed to pry some new information out of the otherwise tight-lipped commander, but something still bothered him. "But why inhibit my Chaos Energy?"

Tower sighed, not liking what he was about to say. "According to my superiors, it is to control powerful individuals. But according to my own observations, it is to destroy the Super form."

...

Shadow found himself staring in amazement at what was happening on the news, a hand to his head as he tried to take in what was going on.

All around the world, people were protesting against the announcement of the new initiative Project: Chaos Control. Some raised signs denouncing GUN, some blocked whole freeways, and a few others dared to burn the GUN flag.

Some familiar faces, including Amy, Omega, and even the Babylon Rogues could be seen often among the sea of protesters, declaring their support for the persecuted.

All three of the Supers stared, barely registering that this was actually happening. They were frozen in shock and awe.

Finally, Shadow snapped out of his trance and stood, resolve hardening his features.

"We can't let this opportunity go to waste," he said, turning to the younger two. "They're protesting for _us_ , they're fighting because they believe we are heroes. We need to take advantage."

The Ultimate Lifeform whipped his head back to the computer. "EVE, are the cameras online?"

"Yes, Shadow," the A.I. answered.

"Good. Hack into all news broadcasting frequencies. Record whatever I say."

...

Once the elevator doors opened, Sonic squinted his eyes at the sudden brightness of the lab. All of the scientists turned at their arrival, standing in respectful silence at their subject.

Commander Tower waited a moment, then stepped into the room, Sonic and the rest of the escort following suit. The stares of the human scientists only made the blue hedgehog even more anxious, and so turned to the Commander.

"So, we Supers are too powerful to be left alone?"

"Yes, according to my superiors," the older human replied. "They feel threatened by the amount of power you and your friends possess, and don't want to risk leaving the power with you when you could easily wipe out continents."

"But we're heroes!" Sonic protested, frustration clearly evident in his tone. "My friends and I would never even _consider_ taking over whole countries just because we can!"

"I know," Tower sighed.

Sonic realized they had stopped, and looked up to find the dreaded machine before him. It looked remarkably similar to the trap Eggman had set up for him when he split the world into pieces and awakened Dark Gaia, with some differences. It was protected by a bowl-like structure, with the same machinery open for him to see. In the center of the machine stood a solid metal chair, with cuffs built in where his wrists, ankles, and torso would be. Surrounding the chair like a shield was a cylindrical glass pod, which was open, and the entire thing was closed off by a similar glass wall, which opened up before the group. Sonic shuddered as his memories of the incident with Eggman and the similar machine came unbidden to his mind. If this was anything like that…

Commander Tower noticed his unease and motioned for the soldiers to take him into the machine.

"The procedure won't last long," he said, staying where he was and looking the blue hero in his emerald green eyes. "It will only take about five minutes to complete, but you will feel a significant amount of pain. Let it run its course, and then it will be all over."

Sonic gulped and nodded, seating himself on the chair. The soldiers took off the handcuffs, then secured him to the machine and left, the glass container closing behind them with a hiss. The blue blur gulped again as his claustrophobia kicked in, finding the space and his being restrained much too restricting for his liking. As the final glass wall sealed itself shut, he could barely make out the GUN Commander's grim face, full of regret, as he heard the first hum of machinery start up…

Then he felt the first wave of pain.

...

The streets were crowded by the hundreds of protesters gathered there, still refusing to back down even though it was early morning. The city square, filled to the brim with angry citizens and peace-keeping officers, displayed on their jumbotrons replays of the GUN announcement condemning the four Supers to imprisonment. As the news footage continued to play, suddenly static seeped into the screen, overtaking the previous broadcast and revealing a darkened room. All of the people below hushed and stopped whatever they were doing, seeming to know something significant was about to happen.

At last, a figure stepped out of the darkness. A black hedgehog with red stripes on his arms, legs, and quills walked up to the screen, ruby red eyes staring at whoever was watching.

"People of Mobius," the deep voice rumbled. "You may have heard some disturbing news about a new GUN initiative called Project: Chaos Control. If you are concerned, saddened, or angry, then you have a right to be."

To his right, another hedgehog stepped forth, silvery white in color and normally wonder-filled golden eyes hardened with seriousness.

"Project: Chaos Control is not meant to just capture Mobians with incredible power," he said, his determination hardening his resolve. "It is meant to destroy that power."

Down below, people gasped and shouted curses to the officials as this new revelation unfolded before them.

"As of now, we are considered the highest-level fugitives at GUN," a female voice spoke up as a purple feline with golden amber eyes revealed herself on the first hedgehog's left. "But there is more."

"We have evaded GUN," the black and red hedgehog pressed. "We have found sanctuary. And now, we have your support."

"People of Mobius," the silvery hedgehog spoke again. "We can't continue to protect you without your help!"

...

Sonic cried out as the energy and the pain laced through his body, permeating every part of him. He clenched his teeth to prevent another scream, but choked back a gasp as he felt something shift in his Chaos Energy. Slowly, as though trying to prevent the inevitable, he felt a small part of his Chaos Energy leave his body, replaced by the unbearable pain that completely enveloped him. He thrashed around in his restraints, too overcome with pain and torment to care about preserving his pride. As the tears rolled down his muzzle, he heard a voice he had hoped beyond hope to never hear again.

 _I've been waiting for you, Controller…_

 _..._

"We seek those willing to stand beside us," Shadow pressed to the enraptured crowd. "We ask for your help. GUN may be out to get us, but we refuse to back down from their challenge."

...

 _It's been so long since we've talked,_ the voice echoed, a smirk clear in its tone as Sonic screamed at a new wave of pain. It laughed haughtily as the blue hedgehog lowered his head, exhausted.

 _My, you've gotten weaker since our last encounter,_ it sneered. _I'm afraid I'll have to remedy that._

"N-no," Sonic gasped, horrified as the images of the voice's previous takeovers filled his mind's eye. Eggman cowering in fright, Amy screaming as the roboticizer activated; Tails, mute with shock at the monster his big brother had become. The Metarex, watching with interest as he lost control at the sight of his scared and injured friends. And the latest, struggling to escape Eggman's trap as Neo Metal Sonic closed in for the kill during the final battle…

...

"Do not be afraid because we are being hunted down," Blaze spoke, calm and collected as ever. "Have courage, because we vow to stand beside you, no matter if the world is our friend or our enemy."

...

"No!" Sonic exclaimed, crying as the negative Chaos Energy singed his navy blue fur.

 _Actually, the correct answer is "yes",_ the voice laughed. _You tried so hard to hold me back, but deep inside you knew one day I would rise again. Well, today's that day. And this time…_

Sonic looked up as he sensed a familiar energy signature. His emerald green eyes widened as he discovered the purple and grey Chaos Emeralds securely attached to the machine overhead.

 _This time I'm here to stay._

 _..._

"We are setting up a network of people willing to support us," Silver said. "No one should be alone in this dark time, and neither should us."

"If you feel you cannot support us directly, then spread the word. Do not let our voice go unheard."

...

"No! You can't-" Sonic choked back a scream, vision blurring. He sensed another shift in Chaos Energy, and recognized the altered energy they had taken from him just before it was shot into the container. The Blue Blur couldn't hold in his screams this time as the altered energy tried to enter his body, tried to neutralize his abilities…

 _I think I've let you suffer enough,_ the voice, so much like his own, pondered. _It's time to bring me back!_

"Y-y-you…" Sonic tried to counter, but the torture was unbearable. The Chaos Emeralds glowed suddenly as negative energy grew in power-and began to alter itself.

...

"We are your heroes. We are your protectors."

...

"Commander, the energy is reversing!" one of the scientists exclaimed from his computer screen. Commander Tower whipped around to speak to him just as another scientist cursed loudly.

"It's rerouting itself into the subject! The level of negative energy is off the charts!"

"The machine can't hold this much energy!" a third yelled.

"Evacuate the base immediately!" Tower commanded. "You six, contain the other subject!"

The soldiers nodded and ran, but as the stairwell doors finally ceased their swinging, Sonic gave one last, tormenting scream. The Commander turned to see what was happening, but everything was engulfed in a brilliant flash of light and a sound of thunder.

...

"We refuse to give in."

...

Mephiles wrung his hands together nervously, at a loss for what to do. Sonic was gone, and his connection to Iblis was cut off. What was he supposed to do now, now that he was little more than a lab rat with an affinity for shadows?

 _Iblis, what do I do?_

The cell door slid open, revealing a squad of soldiers rushing into his cell with cuffs at the ready.

The shade backed away, caught off-guard. "What is the meaning of this?"

One of the soldiers opened his mouth to remind the shade who was in control when a rumbling sound rocked the building, effectively slowing down the soldiers' advance. Just as each person glanced to each other, looking for an explanation, a violent explosion sent everyone and everything flying.

...

The lab was covered in smoke and debris, an occasional fire flickering and casting confusing shadows on the walls. Out of the ruins of what was once a feared mechanical wonder, a lone figure stood to his feet. He blended easily into the shadows, making it hard to discern a trick of the light from flesh and bone. However, if one were to be watching the entire scene, they could never mistake the glow of the figure's pure white eyes.

...

Hands joined together, raised for the crowd to see, as the three Supers made their declaration known.

"We are The Resistance!"

...

Smoke was everywhere, only helping to further annoy the shade as he finally regained consciousness. He groaned and tried to rise, only to get on his hands and knees before the pain in his head forced him to stop. He looked around at the ruins of what was once his cell, finding it satisfying that the soldiers were gone.

 _How long have I been unconscious?_ he wondered. _A few minutes? Nearly an hour?_

He glanced toward the door, surprised but satisfied to find it wide open. He started towards it, but only made it a few steps before his ankle chain grew taut much sooner than before. Mephiles turned, and cursed as he realized a large beam had fallen on the chain, further restricting his movement. He turned around to evaluate it and figure out how to break free, but stopped as he heard a faint voice calling his name.

 _Mephiles…_

Where was it coming from?

 _Mephiles…_

"Who's there?!" The demigod whirled around, forgetting his dilemma as he tried to locate the sound.

"Mephiles…"

The shade turned to the doorway. A large figure stood there, his massive frame almost dwarfing the way to freedom.

Mephiles squinted his reptilian green eyes, trying to make it out, before those green eyes widened with shock.

"Iblis?"

"Yes," the deep voice replied, clearer now. "...And no."

Mephiles screamed as his brother fell at his feet, landing on the cold floor with a dull _thump_. The shade backed away as far as his tether would allow, a hand clutched to his chest in pure terror.

His brother was covered in blood, something the shade hadn't thought was possible. His green eyes, once full of rage and fire, now stared blindly ahead, nothing more than cold embers.

"It's been so long since I've killed," the voice spoke again, clearly not Iblis as its owner stood in the doorway, taking a few steps into the cell. "I wonder what kind of fight you'll offer to entertain me…"

Mephiles looked up, tears beginning to form. "W-why… why did…" Then, his poison green eyes hardened into obsidian, his shock giving way to rage as he stood.

"Y-you killed him! You killed Brother!" he screamed, fists clenched and ears laid back and flattened against his head. He hated how childlike he sounded, but he couldn't allow himself to dwell on his weakness. His brother's murderer had to be brought to justice, he had to-

His tail involuntarily curled between his legs as his brother's murderer laughed haughtily.

"Yes, I did."

The figure was gone in a flash. Mephiles whipped wildly around, trying to locate his foe. Unfortunately, it was his foe who struck first.

He cried out as a foot kicked him in the back, then gasped as said foot struck him in the stomach. He tried to swing a fist, only to be backhanded and thrown to the ground. The shade scrabbled as far away from his adversary as he could, only to be grabbed by the still active inhibitor collar and lifted up to face the pure-white eyes of his brother's killer.

"My, my, is this any way to greet the great Dark Sonic?"

 **Part 1 of 3.**

 ***insert fangirl screaming here***

 **... I have no words. I feel sorry for these characters but at the same time... it's for the good of the plot. And the good of you guys, as well.**

 **Special thanks to my betareader, silvershadowlover on deviantart, for coming up with the idea of bringing Dark Sonic into the mix. I wouldn't have thought of it myself!**

 **Chapter 6 will be posted in about two weeks from today (providing work doesn't get in the way). Till then, have a good day, and kindly leave a review. It really helps!**


	6. Chapter 6: Found

***Unlocks barred windows and breathes in the fresh air***

 **YES! I HAVE RETURNED! ON HALLOWEEN, NO LESS! MWAHAHAHAHA!**

 **I am so very sorry, everyone, for leaving you hanging for the last... month? Dang, I'm really sorry about that. School and work have been whooping my butt for the past few weeks, and I haven't been able to update this story in that time. It was difficult enough writing this chapter, let alone edit it! Oh, and btw, this chapter is unbetaed, so please let me know if you see something wonky in the pacing or writing. Both me and my betareader are very busy right now, so I can't say for sure when the next chapter will come out. Definitely before November ends, but I really don't know.**

 **On another note, I named all the chapters! Be sure to look at these carefully thought-up name for the chapters, I may or may not keep this up, so please let me know if you like this.**

 **Anyway, enough of my excuses and rambling...**

Project: Chaos Control

Chapter 6

Found

Shadow watched the computer screens with calm interest, finally earning a quiet moment after he sent the other two Supers to rest in one of the many rooms of the former Eggman base.

News of the Resistance traveled fast. Almost as soon as that first message ended, EVE reported a slew of support coming in from all around the globe. Some were spreading the word, some were sending donations, and some even volunteered their services toward the cause. Amy Rose and Tails were busy conducting the outpouring of support, trying to organize all the volunteers, while EVE recorded all the financial aspects.

Shadow merely shook his head in wonderment, at a loss for words. He remembered at one point he believed it was him against the world, everyone out to get him. He could still recall that one instance where Mephiles had told him his fate in an alternate future, where he was hunted down for unleashing chaos around the world and promptly sealed away. He had believed the shade then, even secretly anticipated the day it came true.

But now, he knew that little demon was wrong. Here was the proof, proof that not all people were bad, proof that not everyone was against him.

If that demon were here now, Shadow wouldn't hesitate to rub it in his mouthless face…

...

The trees passed by in a blur, the early morning light too faint yet to illuminate the shadows of the dying night. The ground underfoot crunched beneath his rocket-soled shoes with fallen leaves and twigs, doing little to hide his fleeing presence. He made little to no sound, but his grey black chest heaved up and down with the exertion of running as far away from his adversary as he could, pausing only to take great chestfuls of air into his protesting lungs. He leaned against a tree now, quivering from quills to tail from his mad dash away from the place of torment-and from the fear that came with being hunted like prey. He bore the cuts and bruises of his adversary's wrath, and had no doubts that worse would come if he let himself get caught again.

He turned his dark grey and teal head wildly, searching for any sign of his pursuer. At first, it seemed like all was normal. Then, he cringed and shuddered as glowing white eyes pierced the darkness to his left, staring him down with something akin to evil excitement. With no other options, he turned and ran in the opposite direction.

...

A four-note ringtone snapped Shadow out of his reverie as EVE's monotone voice filled the silence.

"Incoming call from GUN communication device. Signal coming from: Club Rouge. Would you like to-"

"Yes, patch it through!"

A moment of silence, then…

"Ebony, do you read me?"

"Loud and clear, Ivory. What's your status?"

"On call. GUN sent me to investigate an explosion in one of their secret research facilities, and I'm on my way there now."

"Do you think…" Shadow didn't dare finish. If he had to retell the story of his failure one more time tonight…

"Who knows? I'll inform you in case anything related to… the Project… comes up."

"Very well," Shadow nodded once, then cut off the transmission. He hated not being out there with his partner, investigating something potentially important to the Resistance's cause. But he had a responsibility to the other two Supers, and until Amy and Tails finished organizing the support, it would be up to him to protect them. There was no one else to fill that role.

The Ultimate Lifeform sighed and held his head in his hands, ears laid back.

 _Rouge, please stay safe…_

 _..._

The fleeing hedgehog stumbled on a root, cursing to himself as the morning chill seeped into his grey-black pelt, sending fresh shudders down his spines.

 _He's coming for me,_ his harried thoughts echoed from within his exhausted and terrified mind. _He killed Brother, he's going to kill me, too. He killed Brother…_

So wrapped up in his fear, he barely recognized the ground giving way underneath his feet before he tumbled down a steep hill, grunting as twigs and branches cut into his already wounded body. His poison green eyes widened as one especially wicked-looking branch seemed to reach out of the blackness, slicing into his eyebrows and blinding him with his own blood. He cried out as he finally landed with a dull thump, all the wind knocked out of him and his right leg throbbing painfully. He curled up out of instinct, quills bristling as he tried desperately to recover from his fall-and knew it was in vain.

 _I can't see,_ he realized with a shudder. _My leg hurts, and I can't hide in the shadows like I should be able to do. The inhibitor collar is still working, meaning I can't fight back or disguise myself… Oh Iblis, what do I do?!_

He curled up tighter into his ball as despair washed over him, waiting with baited breath for whatever torture was about to-

"M-Mephiles?"

He stiffened at the sound of his name, caught off guard at the concern and shock in the voice that hovered over his terrified form. He vaguely felt a gloved hand light itself on his forehead as he realized the voice was female.

...

A shadowy figure watched the scene below him with a glare, his blue-black quills bristling with rage. This was certainly not the turn of events he had been expecting. The little whelp was supposed to be alone, whimpering like the cowardly dog he was. He wasn't supposed to be found, nevermind by the Resistance he had heard rumors of through the comlink he had stolen from GUN. He knew Rouge was close to Shadow, so it would come to no surprise if she-

 _Yup,_ he thought, suspicions confirmed, as the bat turned on her comlink and requested for help, never taking her hand off of the shade. _Typical of Team Dark. Always calling the shots. If only I had steered him back towards the facility, then maybe I could've had a little more time to enjoy throwing him around…_

A sudden idea struck the hedgehog, the brilliance behind such a thought causing his once heroic smirk to widen into a predator's grin.

 _No, he won't be the only one,_ he chuckled softly as a flash of light briefly illuminated the surrounding trees, announcing the arrival of a certain Ultimate Lifeform. He watched as the two agents argued with one another, gesturing to the quivering whelp a few times, before Shadow finally grumbled defeat and carefully lifted the wounded hedgehog by his legs and shoulders.

 _Let them have my pet. He will be my messenger, and when the time is right…_

A deep rumbling voice, followed by another flash of light, and it was as if the three had never been there.

… _I will strike._

 _..._

The shade lay still, groaning as he finally regained consciousness. He was lying on something soft and comfortable, so different from the metal bench he had been forced to sleep on during his captivity in GUN. He vaguely recognized a blanket had been thrown over his battered body up to his chest, and his arms were exposed to the cold air. He tried to blink, but quickly realized that bandages covered his eyes and forehead, effectively blindfolding him. Panicking at his vulnerability, he reached up to remove them- only to have gloved hands clasp his wrists suddenly, firmly but gently bringing them down.

"Hey, calm down," a gruff voice said, and Mephiles winced when he recognized it as Shadow's. "Those need to stay on for a few days."

His ears flattened themselves to his head, a growl resounding in his throat despite his uncertainty.

"Where am I?"

"In a secret bunker belonging to the Resistance."

The demigod cocked an ear, curiosity perking. "A Resistance… against GUN, I presume?"

"No," came the curt reply. "Against Project: Chaos Control. I have no qualms with the soldiers, only the initiative."

 _Typical of the Ultimate Lifeform..._

He grunted and turned his head away, absorbing this new information. He did vaguely recall someone had picked him up (he presumed it was Shadow, remembering the reluctance in his movements), saying something about a base, before he had passed out from exhaustion. He gently ran his hand along the bandages, following its path behind his head-

His thumb came into contact with the inhibitor collar.

He hissed vehemently when he realized he was still collared, and wrapped his fingers around the metal band, fully intending on ripping it off. Before he could do so, however, Shadow once again grabbed his wrists and roughly pinned them down, a growl rumbling from his own throat.

"Stop," he barked, only gripping tighter as the shade tried to pull his hands free. "I'm not going to tolerate this anymore! If I have to restrain you to that bed, I will!"

"N-no," Mephiles gasped, remembering the pain and humiliation the dreaded collar had brought during his captivity. Then, in his mind's eye, he saw the glowing white eyes, staring at him with an evil smirk. He shuddered as he recalled the hate, the pain, and the death. So much death…

 _Brother…_

"Snap out of it!" Shadow yelled, effectively bringing the shade out of his nightmare. He flinched and seemed to grow smaller, quivering uncontrollably as the fear lingered. He felt his arch enemy's gloved hand on his shoulder, trying in vain to shake him.

"You were too late."

Shadow narrowed his gaze, fists tightening their grip on the shade. "What?!"

"You were too late. I talked with him, before they took him for his procedure. He's gone now. You failed-"

The shade felt his arch rival lean in closer, almost literally feeling the rage coming off of the Ultimate Lifeform in waves.

"What. _Happened_?!" The Ultimate Lifeform demanded, his already-thin patience threatening to shatter. After taking the demon to the clinic, Rouge had demanded she go back to the ruined facility to finish her investigation. She had yet to return, and if she came back, only to tell him that they had committed the ultimate failure to save the world's hero...

"Dark…" the shade gasped, snapping Shadow back to the present. He turned his attention back to Mephiles, realizing with shock that his most hated enemy was failing to hide his fear as he whispered three ominous words.

"Dark is coming."

...

 **I am so mean! Hopefully the next chapter won't take as long to get up.**

 **Anyway, hope you enjoyed this chapter and pretty please leave a review. You don't know how meaningful each new review is!**

 **Well, until next time, hope you have a happy Halloween!**


	7. Chapter 7: Shells

**Hello, everyone. So very sorry for the long wait for this chapter. I blame writer's block and school. Plus, I didn't actually have a plan for how this chapter would turn out... (beats myself over the head with a stick for taking so long). Anyway, here's your long overdue chapter!**

Project: Chaos Control

Chapter 7

Shells

Snowflakes danced within the flurry of wind, blowing against the hills and mountainsides as they careened into what seemed to be solid metal walls camouflaged to look like the rocks surrounding them. The never-ending whiteness made it near impossible to tell what time of day it was, nevermind where exactly this place was. Within the metal walls, however, one refugee knew all too well.

In one room of the secret bunker, a lone hedgehog sat hunched over a desk, staring at a blank piece of paper with a pencil in hand. His normally stoic ruby red eyes bore in full view all the guilt and all the weight of responsibility on his shoulders, and for a moment he seemed even afraid to write. However, the hard gleam of determination returned, and after taking a moment to gather his thoughts, he finally brought down the pencil and began to write.

 _Dear Maria,_

 _Remember what Rouge told me last night? Well, it came true. Project: Chaos Control is now official. I and the others are now in hiding, safe from GUN for the moment._

 _Well, not all of us. Silver and Blaze are with me, but Sonic… he's gone. Taken by GUN, before I could get to him. Remember the attack on the ARK? I feel just as guilty about Sonic's capture as I did when I watched you bleed to death. I can't help but feel as if I could have done something more to keep that Faker out of harm's way, but… there's nothing I can do now. If Rouge's last bit of information is correct, then it really is too late to save him. By the time we find him again, he would be…_

 _I don't want to even think about it, Maria. To see him weak, powerless, and_ normal _… I hope you understand. It is simply too strange, and I would hate to look into his eyes and admit to him that I couldn't even-_

The hedgehog stopped, taking a moment to collect himself. This letter was more emotional than he had intended, but hadn't Rouge said that these letters were supposed to be that way? Maybe he should talk about something else.

 _Sorry, I can't finish that thought. It hurts too much. But, there's something else I need to tell you before I go._

 _Remember the final battle? Yes, perhaps looking back the letter describing that sounded more like a report than a private letter, but I digress._

 _Well, do you remember that demon, Mephiles? Well, Rouge was on a mission for GUN when she found him. I refused to believe what I saw at first, but I had no choice but to accept it. He was curled up in a forest at the foot of a steep hill, shivering uncontrollably. Cuts and bruises littered his body, and I saw one especially bad cut just above his eyes was bleeding bad enough to blind him. Rouge was there with him, and for a moment I…_

 _To tell you the truth, Maria, I didn't want to do anything with him. GUN would go after him once they find out he has escaped, and if they know we helped him… I fear we would be branded traitors as well as dangers to the public. But, that's not all._

 _Maria, I_ hate _him. I know you would cringe and scold me for using such a strong word, but it's true. I hate him with all my being. I would never admit this anywhere else, but… he is just like me in some respects. Yet, how could someone so similar to me become so twisted and evil? I hate that about him, so I tried to tell Rouge to leave him, since GUN would come for him soon enough._

 _You would be proud of her, Maria, because she gave a… rather convincing argument. Not that I have enough guilt as it is. And so, that's how I ended up hovering over my enemy's bedside, waiting for him to wake so that I could interrogate him. That was perhaps the most humiliating thing to happen to me; well, aside from the time Faker threw a party for my 50th birthday…_

 _Maria, something happened to Mephiles during his time in GUN custody. I don't know what they did, but he's... (I can't even wrap my head around this)..._ scared _. I never thought that I would ever see that demon scared of anything, not even of death. But this… Dark, he spoke of… it must be a threat. He could barely lay still, he even tried to get off of the bed and run, he was so scared. I don't know what to do with him, maybe the others could help. I'm numb to him at the moment._

 _But he knows what happened to Sonic. I can't ignore that. I'll wake the others and actually interrogate him in the morning. At this point, any information helps._

 _Well, this is the end of my letter. I hope you get this, and… thank you for listening._

 _Shadow._

 _..._

She heard the soothing scratching of pencil on paper, heard every sigh of frustration and exhaustion. She vaguely sensed the brief surge of energy when he used Chaos Control, and felt it again barely a minute later when he returned. The lilac feline slowly opened a golden amber eye, catching the attention of the Ultimate Lifeform.

Shadow turned toward her as she lifted herself off of the bed, face carefully neutral. In the other bed, Silver remained curled up within the sheets, obviously fast asleep.

"Anything new?" Blaze asked, shrugging away the sheets from herself and reaching for her coat.

The scoff the imposing hedgehog gave as a reply caused her to look up into his ruby red eyes.

"You have no idea…" he said, glancing away as if debating something.

Blaze opened her mouth to question the look, but before she could utter a word, Silver groaned and lifted himself off of the bed, rubbing his tired eyes.

"Wh-whazzup?" he yawned, running a hand through his long quills. "What time is it?"

"I believe almost eight-thirty in the morning."

"Wait, that early? Nevermind, I'll just go back to bed and-"

"Not yet," Shadow's voice cut in, sudden urgency present in his tone. "Mephiles the Dark is now in our custody."

Blaze instantly froze, the implications behind those words raising the hair on the back of her neck. She glanced back at the Ultimate Lifeform, shocked to see the soldier actually show mixed feelings over what he had just said.

Silver stared blankly at Shadow before giving a nervous laugh, much to Shadow's chagrin.

"Heheh, nice one, Shad. Now what's _really_ going on?"

"Nothing short of what I just said. Mephiles is our prisoner now," he put bluntly, ripping the metaphorical Band-Aid off.

"Prisoner?" Blaze spoke up, careful to reign in her emotions. "Do you mean to say that-"

"He didn't attack me, if that's what you two are thinking," he replied glancing from Blaze to Silver then back again. "But something attacked _him_ , powerful enough to wound him. Plus, he knows what happened to Sonic."

Blaze couldn't shake the feeling that he was trying to convince _himself_ of what he was saying, but decided to save that observation for later. Now was not the time for doubts.

"Where is he now?"

"In the clinic, temporarily blind and restrained to the bed." The fiery feline missed the slightest hint of worry at the edge of Shadow's tone.

"C-can we see him?"

Blaze shot a concerned glance in Silver's direction, all too aware of his fear and naivety. Despite his incredible power, the silver hedgehog was still vulnerable at the core. And since Mephiles was a master of deception and manipulation…

 _No, Soleanna won't happen again. If that demon tries something, I will protect Silver till the very end. Besides, with Shadow there, he won't even have an opportunity to attack._

 _... Won't he?_

"I was just about to go interrogate him," Shadow replied, snapping Blaze back to the present. "You can come if you want, but he's not the threat at the moment. You'll see why..."

...

The floating island stood as a black outline against the near blinding light of the rising sun, hailing the birth of a new day. The last remaining stars winked weakly, as one by one they disappeared in the face of the bigger star until only one was left, glittering in the reflective surface of a giant green emerald that glowed with its own radiance.

A pair of purple eyes stared deeply into the glowing surface of the giant emerald, peering inside as if looking for some change deep within the jewel's depths and outright oblivious to the passage of time around him. The lines under his eyes gave away the fact that the watcher hadn't slept at all these last twenty-four hours, yet the determined gleam never left eyes, nor did his leaning frame change in the slightest. The spiked hands that propped his still body against the gem as he leaned forward remained curled into fists, as if this arduous task was trying at his already thin patience-if one could call it that.

Instead, only a small sigh escaped his pursed lips, the slightest tilting of his head the first movement he had made in hours. His eyebrows creased, worry and fear etched into his features, as he whispered fervently.

"Master Emerald, heed my plea. When Shadow called, he wouldn't answer my questions about my… friend, and I need to know if what I fear is true or not. Show me Sonic, show me he is safe. Please…"

For a moment, nothing happened.

Then the great emerald glowed radiantly, far brighter than before. The guardian took a step back, raising a gloved fist to shield his violet eyes from the light. When it dimmed somewhat a few moments later, he swiftly closed the distance, completely enraptured by the reaction he got.

"Wh-what do you mean…?" he rasped, suddenly sounding much older than his seventeen years of age. "Master Emerald, please… what is this darkness that is coming? What happened to Sonic? Please…"

The emerald glowed stronger again, not blinding like before. Instead, this reaction seemed to be giving off comfort, or at least something close to that. The red echidna seemed to relax under this new warmth emanating from the gem, but his heart remained heavy.

"How will we survive this... if…"

The question remained unspoken, as a sudden new light burned within his eyes along with another strong glow from within the Master Emerald. He straightened up, standing firm as a refreshed resolve lent new strength to his tired body.

"The servers…. The servers are the seven Chaos… Chaos is the power enriched by the heart… The Controll _ers_ exist to unify the Chaos…."

 _The four Controllers, joined by a fifth…_

 _..._

"Man, you weren't kidding," Silver gasped, peering through the one-way window into the only occupied clinic room. Inside, Shadow's most hated enemy swept his bandaged head around the room, trying desperately to pinpoint _something_ familiar without the use of his blindfolded eyes. His ears swiveled in every direction as he tugged at the restraints pinning him to the bed, barely keeping from having a full-blown panic attack. The sight left a bitter taste in the time traveler's mouth.

"Whatever did this to him…"

"... Has to be a threat," Blaze finished, an indiscernible frown on her face. Her ears strained forward, and her frown deepened. "He's panicking," she stated. "Saying something about being too late, too weak, to save-"

She froze suddenly, backing slowly away from the window as her normally stoic mask crumbled for a moment. Her words came out as only a small whisper as she shared her revelation.

"Iblis is dead."

"Wh-what?!" Silver gasped, too shocked to say anything else. "I thought Iblis was immortal!"

"Not anymore," Blaze replied, recovering from the shock. "I'm trying to detect his Chaos Aura, but I can't feel anything at the moment."

"And if Meph has that twin thing going on…"

"... Then it must be true," Shadow cut in, breaking his silence. He turned and reached for the door that would let him into his rival's room. "Are you two coming or not?"

Silver glanced at Blaze, noting her determined glare, before nodding.

"Let's do it."

The door swung inward with the faintest sound of a creak, but it was just enough to alert the lone occupant of their presences. Silver entered to find Mephiles turned in their direction, ears strained forward to catch the sound of their footfalls.

To Silver it was extremely hard to tell what the shade was thinking at this point. But one glance at Blaze's thoughtful and somewhat relieved expression assured him that an impending attack was out of the question-for the moment at least. As Shadow moved closer to the (insert choking noise) helpless prisoner, Silver couldn't grasp that the Mephiles he was used to had been broken down into this frightened shell of a person. As the former demigod tried to shift away from the others' direction, only to give off a faint whimper as the restraints held him in place, Silver felt that bitter taste return to his mouth, further intensifying the sick feeling roiling in his gut.

 _Whatever did this to him… better watch its back. We'll find it, and we'll stop it before anyone else gets hurt. I swear..._

 _..._

Barely a half-hour later, Shadow threw the door open as he exited the one-way room, the steam from his anger and frustration almost smoking off of his body. Silver followed on his heels, struggling to catch up to the steaming hedgehog.

"Sh-Shadow, wait!" the younger gasped, stumbling on his own two feet.

"That demon thinks he can keep that secret from me…" the Ultimate Lifeform growled to no one in particular, turning the corner to enter a different set of hallways. He continued to skate/stomp down multiple corridors, pausing only to enter the computer room. Once inside, he rushed to the keypad and after typing a certain number, he leaned back and waited rather impatiently for some response. Sure enough, the form of a certain two-tailed genius appeared on the screen.

"Shadow? What going on?"

"I have a lead on where they took Sonic," Shadow stated, cutting to the chase. "But the person who possesses this information is unwilling to give it up. I need you to craft a machine, one that will allow me to access his memories…"

Silver tried to keep up, but the icy burning in his chest forced him to stop. Gasping for air, he leaned against the wall just around the corner and closed his golden eyes, thinking back on the interrogation.

 _He never told us who Dark was,_ the time traveler reflected. _Just said that he was coming to finish him off. He kept trying to get away, so I guess that's why Shadow had to restrain him like that…_

 _But, I can't believe GUN actually took away some of his powers! And we didn't even figure it out until Blaze spoke up about it-_

"Silver?"

And speaking of…

Silver turned as Blaze appeared where he came from, looking a lot less winded than him, like she just came back from a light jog. She walked up to him, hands on her hips and a curious gleam in her beautiful golden amber eyes.

"Where did Shadow go?"

"Computer... (huff)... room… (huff). Dunno… why…."

"Probably contacting Rouge," Blaze stated. "Perhaps to ask for more information."

"Right," Silver scratched the back of his head. "Hey, how did you know that Mephiles was depowered? Shadow and I couldn't really tell until you asked him."

"His entire behavior screamed weak and defenseless, akin to prey," Blaze replied, tail flicking back and forth. "At first I thought he was acting that way because he was blinded and unable to escape. But the more I thought about it and the more I watched him, I realized he never tried to use his powers. It was as if he had given up."

"And, Iblis…?"

"Dead," Blaze looked away, hiding the strange sorrow that threatened to break through her stoic shell. "When Shadow left, I asked him about Iblis' missing Aura. He… he saw the body. He's gone."

"And that's good, right? I mean, no more eternal fire elemental to turn the future into a fiery wasteland again. No more Solaris to wreck the timeline!"

"Silver," Blaze sighed, shaking her head. "I don't think that's the point. As evil as he is, Mephiles just lost a lot of his power and his entire family, if you can call them that. His proud identity has been utterly shattered, and now he is wounded, in a strange place, among his enemies, blind and unable to escape or lash out at anyone that comes close. And all of that is overshadowed by his fear of this, _Dark_ he keeps whimpering about."

Silver looked into Blaze's eyes, and could see the questions raging inside. The one thing about Dark they were able to figure out was that he was a threat, nothing more. No description, no elaboration. Nothing. It was maddening.

For Silver, at least.

"Why do you think he won't tell us who Dark is, or what he looks like? I'm really confused…"

"I don't think he can say for sure, because he might not know much about Dark other than the fact that he is something to fear. Perhaps that is the name given to him at the time of their meeting, or perhaps it is something he has come to associate with GUN and the experiments. Either way, he is keeping that knowledge from us for a reason.

"... And I intend to find the secret hiding in his shell."

...

Unending darkness surrounded him, parting only before his glowing white eyes as he paced restlessly, waiting for some unspoken command. He growled low, patience running thinner and thinner until he let out a roar and upturned the small bedside drawer that was sitting innocently within striking distance to his left. He let out a puff of air and calmed down considerably, although the rage still boiled underneath his skin.

 _How long is this going to take?_ He thought, frustration clawing into his train of thought. _It's only been a few hours; he_ should've _told them about me by now. I should_ know _it if he does; that weakling could barely keep his mouth shut when I-_

"Dark," an overhead mechanical voice cut through his train of thought, turning his eyes from pupil-less glowing white to emerald green in the span of a heartbeat. "The Commander will see you now."

"About damn time, it's already noon," Dark Sonic grumbled, righting the small dresser and reaching for the door. Before he opened it, however, he paused and allowed a small smirk to play on his lips.

 _Time's running out for you,too, runt. You better tell them, and watch your back, cuz I got an ace up my sleeve._

As he opened the door, the light that entered his room illuminated the new combat suit the former hero was wearing, and the crest knit into the shoulder pad.

The very crest of a GUN soldier.

 **I promise, the rest of the chapters will never have this long a wait again! The rest are already planned out, and I should be getting another chapter up sometime by the end of this month. **

**Until then, please leave a review. I really appreciate it that Frentic Kinetic and Zosonils have been diligently reviewing each chapter, you guys are the best! However, I have 15 other followers whom I haven't heard from at all. If you're reading this, and you aren't one of the above, then please leave a review telling me what you think of this story. I really want to know what is it that you love about this story, or like enough to follow. Pretty please? You don't know how much this will help!**

 **Anyway, hope y'all are having a good day!**


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